INRENA (El Instituto Nacional de Recursos Naturales), the official body with general oversight of Peru's national resources, reported in August 2005 that the Peruvian government was considering a recommendation to close the Inca Trail for three months from January to March during the rainy season in order to reduce erosion and allow time for maintenance work. There seems to be very little of an official nature in English about the proposal but if you can read Spanish have a look at the web page below. (My Spanish is not very good but I can get the general idea).
Boletín de Noticias No. 598 El Medio al servicio del Ambiente
http://www.inrena.gob.pe/comunicaciones/boletin/bn0508/bn050810.pdfThere is also an item from the Reuters news agency at the web page below (again in Spanish) which says the proposal comes from El Ministerio de Comercio Exterior y Turismo (the Ministry of Foreign trade and Tourism).
Perú propone cerrar Camino Inca tres meses al año por lluvias
http://www.invertia.com/noticias/noticia.asp?idnoticia=1340622However I have not seen anything yet about a decision having been taken. I suspect it is still under consideration.
Roy